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Song F, Hou C, Huang Y, Liang J, Cai H, Tian G, Jiang Y, Wang Z, Hou J. Lactylome analyses suggest systematic lysine-lactylated substrates in oral squamous cell carcinoma under normoxia and hypoxia. Cell Signal 2024; 120:111228. [PMID: 38750680 DOI: 10.1016/j.cellsig.2024.111228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/05/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Cancer cells tend to live in hypoxic environment characterized by enhanced glycolysis and accumulation of lactate. Intracellular lactate is shown to drive a novel type of post-translational modification (PTM), lysine lactylation (Kla). Kla has been confirmed to affect the malignant progression of tumors such as hepatocellular carcinoma (HCC) and colon cancer, whereas the global lactylomic profiling of oral squamous cell carcinoma (OSCC) is unclear. Here, the integrative lactylome and proteome analyses by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 1011 Kla sites within 532 proteins and 1197 Kla sites within 608 proteins in SCC25 cells under normoxic and hypoxic environments, respectively. Among these lactylated proteins, histones accounted for only a small fraction, suggesting the presence of Kla modification of OSCC in a large number of non-histone proteins. Notably, Kla preferred to enrich in spliceosome, ribosome and glycolysis/gluconeogenesis pathway in both normoxic and hypoxic cultures. Compared with normoxia, 589 differential proteins with 898 differentially lactylated sites were detected under hypoxia, which were mainly associated with the glycolysis/gluconeogenesis pathway by KEGG analysis. Importantly, we verified the presence of lactylation modification in the spliceosomal proteins hnRNPA1, SF3A1, hnRNPU and SLU7, as well as in glycolytic enzyme PFKP. In addition, the differential alternative splicing analysis described the divergence of pre-mRNA splicing patterns in the presence or absence of sodium lactate and at different oxygen concentrations. Finally, a negative correlation between tissue Kla levels and the prognosis of OSCC patients was revealed by immunohistochemistry. Our study is the first report to elucidate the lactylome and its biological function in OSCC, which deepens our understanding of the mechanisms underlying OSCC progression and provides a novel strategy for targeted therapy for OSCC.
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Affiliation(s)
- Fan Song
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Chen Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Yingzhao Huang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Jianfeng Liang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Hongshi Cai
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Guoli Tian
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Yaoqi Jiang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Ziyi Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China
| | - Jinsong Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China; Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510055, China.
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Singh AK, Upadhyay V, Sethi A, Chowdhury S, Mishra S, Verma SP, Bhatt MLB, Trivedi AK. Ring finger protein 138 inhibits transcription factor C/EBPα protein turnover leading to differentiation arrest in acute myeloid leukemia. Biochem J 2024; 481:653-666. [PMID: 38666590 DOI: 10.1042/bcj20240027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024]
Abstract
E3 ubiquitin ligase, ring finger protein 138 (RNF138) is involved in several biological processes; however, its role in myeloid differentiation or tumorigenesis remains unclear. RNAseq data from TNMplot showed that RNF138 mRNA levels are highly elevated in acute myeloid leukemia (AML) bone marrow samples as compared with bone marrow of normal volunteers. Here, we show that RNF138 serves as an E3 ligase for the tumor suppressor CCAAT/enhancer binding protein (C/EBPα) and promotes its degradation leading to myeloid differentiation arrest in AML. Wild-type RNF138 physically interacts with C/EBPα and promotes its ubiquitin-dependent proteasome degradation while a mutant RNF-138 deficient in ligase activity though interacts with C/EBPα, fails to down-regulate it. We show that RNF138 depletion enhances endogenous C/EBPα levels in peripheral blood mononuclear cells (PBMCs) isolated from healthy volunteers. Our data further shows that RNF138-mediated degradation of C/EBPα negatively affects its transactivation potential on its target genes. Furthermore, RNF138 overexpression inhibits all-trans-retinoic acid-induced differentiation of HL-60 cells whereas RNF138 RNAi enhances. In line with RNF138 inhibiting C/EBPα protein turnover, we also observed that RNF138 overexpression inhibited β-estradiol (E2)-induced C/EBPα driven granulocytic differentiation in C/EBPα inducible K562-p42C/EBPα-estrogen receptor cells. Furthermore, we also recapitulated these findings in PBMCs isolated from AML patients where depletion of RNF138 increased the expression of myeloid differentiation marker CD11b. These results suggest that RNF138 inhibits myeloid differentiation by targeting C/EBPα for proteasomal degradation and may provide a plausible mechanism for loss of C/EBPα expression often observed in myeloid leukemia. Also, targeting RNF138 may resolve differentiation arrest by restoring C/EBPα expression in AML.
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Affiliation(s)
- Anil Kumar Singh
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, UP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishal Upadhyay
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, UP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Arppita Sethi
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, UP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sangita Chowdhury
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, UP, India
| | - Shivkant Mishra
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, UP, India
| | - Shailendra Prasad Verma
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, UP, India
- King George's Medical University, Lucknow 226003, UP, India
| | | | - Arun Kumar Trivedi
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, UP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Upadhyay V, Singh AK, Sharma S, Sethi A, Srivastava S, Chowdhury S, Siddiqui S, Chattopadhyay N, Trivedi AK. RING finger E3 ligase, RNF138 inhibits osteoblast differentiation by negatively regulating Runx2 protein turnover. J Cell Physiol 2024; 239:e31217. [PMID: 38327035 DOI: 10.1002/jcp.31217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
A few ubiquitin ligases have been shown to target Runx2, the key osteogenic transcription factor and thereby regulate bone formation. The regulation of Runx2 expression and function are controlled both at the transcriptional and posttranslational levels. Really interesting new gene (RING) finger ubiquitin ligases of which RNF138 is a member are important players in the ubiquitin-proteasome system, contributing to the regulation of protein turnover and cellular processes. Here, we demonstrated that RNF138 negatively correlated with Runx2 protein levels in osteopenic ovariectomized rats which implied its role in bone loss. Accordingly, RNF138 overexpression potently inhibited osteoblast differentiation of mesenchyme-like C3H10T1/2 as well primary rat calvarial osteoblast (RCO) cells in vitro, whereas overexpression of catalytically inactive mutant RNF138Δ18-58 (lacks RING finger domain) had mild to no effect. Contrarily, RNF138 depletion copiously enhanced endogenous Runx2 levels and augmented osteogenic differentiation of C3H10T1/2 as well as RCOs. Mechanistically, RNF138 physically associates within multiple regions of Runx2 and ubiquitinates it leading to its reduced protein stability in a proteasome-dependent manner. Moreover, catalytically active RNF138 destabilized Runx2 which resulted in inhibition of its transactivation potential and physiological function of promoting osteoblast differentiation leading to bone loss. These findings underscore the functional involvement of RNF138 in bone formation which is primarily achieved through its modulation of Runx2 by stimulating ubiquitin-mediated proteasomal degradation. Thus, our findings indicate that RNF138 could be a promising novel target for therapeutic intervention in postmenopausal osteoporosis.
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Affiliation(s)
- Vishal Upadhyay
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anil Kumar Singh
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shivani Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
| | - Arppita Sethi
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Swati Srivastava
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
| | - Sangita Chowdhury
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shumaila Siddiqui
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Naibedya Chattopadhyay
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
| | - Arun Kumar Trivedi
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Utter Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Chen G, Gao X, Jia X, Wang Y, Xu L, Yu D, Chang S, Deng H, Hu K, Wang G, Li B, Xu Z, Lu Y, Wang H, Zhang T, Song D, Yang G, Wu X, Zhu H, Zhu W, Shi J. Ribosomal protein S3 mediates drug resistance of proteasome inhibitor: potential therapeutic application in multiple myeloma. Haematologica 2024; 109:1206-1219. [PMID: 37767568 PMCID: PMC10985453 DOI: 10.3324/haematol.2023.282789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Multiple myeloma (MM) remains incurable due to drug resistance. Ribosomal protein S3 (RPS3) has been identified as a non-Rel subunit of NF-κB. However, the detailed biological roles of RPS3 remain unclear. Here, we report for the first time that RPS3 is necessary for MM survival and drug resistance. RPS3 was highly expressed in MM, and knockout of RPS3 in MM inhibited cell growth and induced cell apoptosis both in vitro and in vivo. Overexpression of RPS3 mediated the proteasome inhibitor resistance of MM and shortened the survival of MM tumor-bearing animals. Moreover, our present study found an interaction between RPS3 and the thyroid hormone receptor interactor 13 (TRIP13), an oncogene related to MM tumorigenesis and drug resistance. We demonstrated that the phosphorylation of RPS3 was mediated by TRIP13 via PKCδ, which played an important role in activating the canonical NF-κB signaling and inducing cell survival and drug resistance in MM. Notably, the inhibition of NF-κB signaling by the small-molecule inhibitor targeting TRIP13, DCZ0415, was capable of triggering synergistic cytotoxicity when combined with bortezomib in drug-resistant MM. This study identifies RPS3 as a novel biomarker and therapeutic target in MM.
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Affiliation(s)
- Gege Chen
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120
| | - Xuejie Gao
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120
| | - Xinyan Jia
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120
| | - Yingcong Wang
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Li Xu
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120
| | - Dandan Yu
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Shuaikang Chang
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120
| | - Hui Deng
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120
| | - Ke Hu
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120
| | - Guanli Wang
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120
| | - Bo Li
- CAS Key Laboratory of Receptor Research; State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research; State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203
| | - Yumeng Lu
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Huaping Wang
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Ting Zhang
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Dongliang Song
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Guang Yang
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Xiaosong Wu
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Huabin Zhu
- Department of Hematology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203.
| | - Jumei Shi
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120.
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5
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Fei X, Zhu C, Liu P, Liu S, Ren L, Lu R, Hou J, Gao Y, Wang X, Pan Y. PELI1: key players in the oncogenic characteristics of pancreatic Cancer. J Exp Clin Cancer Res 2024; 43:91. [PMID: 38528516 PMCID: PMC10962118 DOI: 10.1186/s13046-024-03008-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/09/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is a highly malignant gastrointestinal tumor, which is characterized by difficulties in early diagnosis, early metastasis, limited therapeutic response and a grim prognosis. Therefore, it is imperative to explore potential therapeutic targets for PC. Currently, although the involvement of the Pellino E3 Ubiquitin Protein Ligase 1 (PELI1) in the human growth of some malignant tumors has been demonstrated, its association with PC remains uncertain. METHODS Bioinformatics, qRT-PCR, Western blot and IHC were used to detect the expression of PELI1 in pancreas or PC tissues and cells at mRNA and protein levels. The effects of PELI1 on the proliferation and metastatic ability of pancreatic cancer in vitro and in vivo were investigated using CCK8, cloning formation, EdU, flow cytometry, IHC, Transwell assay, wound healing, nude mice subcutaneous tumorigenesis and intrasplenic injection to construct a liver metastasis model. The interactions of PELI1 with proteins as well as the main functions and pathways were investigated by protein profiling, Co-IP, GST-pull down, Immunofluorescence techniques, immunohistochemical co-localization and enrichment analysis. The rescue experiment verified the above experimental results. RESULTS The mRNA and protein expression levels of PELI1 in PC tissues were upregulated and were associated with poor prognosis of patients, in vitro and in vivo experiments confirmed that PELI1 can affect the proliferation and metastatic ability of PC cells. Co-IP, GST-pull down, and other experiments found that PELI1 interacted with Ribosomal Protein S3 (RPS3) through the FHA structural domain and promoted the polyubiquitination of RPS3 in the K48 chain, thereby activates the PI3K/Akt/GSK3β signaling pathway. Moreover, ubiquitinated degradation of RPS3 further reduces Tumor Protein P53 (p53) protein stability and increases p53 degradation by MDM2 Proto-Oncogene (MDM2). CONCLUSION PELI1 is overexpressed in PC, which increased ubiquitination of RPS3 proteins and activates the PI3K/Akt/GSK3β signaling pathway, as well as reduces the protective effect of RPS3 on p53 and promotes the degradation of the p53 protein, which facilitates the progression of PC and leads to a poor prognosis for patients. Therefore, PELI1 is a potential target for the treatment of PC.
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Affiliation(s)
- Xiaobin Fei
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Changhao Zhu
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Peng Liu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Songbai Liu
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
- Department of Hepatobiliary Surgery, Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Likun Ren
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Rishang Lu
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Junyi Hou
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Yongjia Gao
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Xing Wang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China.
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China.
| | - Yaozhen Pan
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China.
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China.
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Locke AJ, Abou Farraj R, Tran C, Zeinali E, Mashayekhi F, Ali JYH, Glover JNM, Ismail IH. The role of RNF138 in DNA end resection is regulated by ubiquitylation and CDK phosphorylation. J Biol Chem 2024; 300:105709. [PMID: 38309501 PMCID: PMC10910129 DOI: 10.1016/j.jbc.2024.105709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/02/2024] [Accepted: 01/18/2024] [Indexed: 02/05/2024] Open
Abstract
Double-strand breaks (DSBs) are DNA lesions that pose a significant threat to genomic stability. The repair of DSBs by the homologous recombination (HR) pathway is preceded by DNA end resection, the 5' to 3' nucleolytic degradation of DNA away from the DSB. We and others previously identified a role for RNF138, a really interesting new gene finger E3 ubiquitin ligase, in stimulating DNA end resection and HR. Yet, little is known about how RNF138's function is regulated in the context of DSB repair. Here, we show that RNF138 is phosphorylated at residue T27 by cyclin-dependent kinase (CDK) activity during the S and G2 phases of the cell cycle. We also observe that RNF138 is ubiquitylated constitutively, with ubiquitylation occurring in part on residue K158 and rising during the S/G2 phases. Interestingly, RNF138 ubiquitylation decreases upon genotoxic stress. By mutating RNF138 at residues T27, K158, and the previously identified S124 ataxia telangiectasia mutated phosphorylation site (Han et al., 2016, ref. 22), we find that post-translational modifications at all three positions mediate DSB repair. Cells expressing the T27A, K158R, and S124A variants of RNF138 are impaired in DNA end resection, HR activity, and are more sensitive to ionizing radiation compared to those expressing wildtype RNF138. Our findings shed more light on how RNF138 activity is controlled by the cell during HR.
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Affiliation(s)
- Andrew J Locke
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Rabih Abou Farraj
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Caroline Tran
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Elham Zeinali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Jana Yasser Hafez Ali
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada; Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
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Jin S, Xiong Y, Zhang W, Qiao H, Wu Y, Jiang S, Fu H. Identification of Candidate Male-Reproduction-Related Genes from the Testis and Androgenic Gland of Macrobrachium nipponense, Regulated by PDHE1, through Transcriptome Profiling Analysis. Int J Mol Sci 2024; 25:1940. [PMID: 38339218 PMCID: PMC10856083 DOI: 10.3390/ijms25031940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The previous publication identified that pyruvate dehydrogenase E1 (PDHE1) positively regulated the process of male reproduction in M. nipponense through affecting the expressions of insulin-like androgenic gland hormone. The present study aimed to identify the potential male-reproduction-related genes that were regulated by PDHE1 through performing the transcriptome profiling analysis in the testis and androgenic gland after the knockdown of the expressions of PDHE1 by the injection of dsPDHE1. Both RNA-Seq and qPCR analysis identified the significant decreases in PDHE1 expressions in the testis and androgenic gland in dsPDHE1-injected prawns compared to those in dsGFP-injected prawns, indicating the efficiency of dsPDHE1 in the present study. Transcriptome profiling analysis identified 56 and 127 differentially expressed genes (DEGs) in the testis and androgenic gland, respectively. KEGG analysis revealed that the energy-metabolism-related pathways represented the main enriched metabolic pathways of DEGs in both the testis and androgenic gland, including pyruvate metabolism, the Citrate cycle (TCA cycle), Glycolysis/Gluconeogenesis, and the Glucagon signaling pathway. Thus, it is predicted that these metabolic pathways and the DEGs from these metabolic pathways regulated by PDHE1 may be involved in the regulation of male reproduction in M. nipponense. Furthermore, four genes were found to be differentially expressed in both the testis and androgenic gland, of which ribosomal protein S3 was down-regulated and uncharacterized protein LOC113829596 was up-regulated in both the testis and androgenic gland in dsPDHE1-injected prawns. The present study provided valuable evidence for the establishment of an artificial technique to regulate the process of male reproduction in M. nipponense.
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Affiliation(s)
- Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Yan Wu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Hongtuo Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
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Liu J, Nagy N, Ayala-Torres C, Aguilar-Alonso F, Morais-Esteves F, Xu S, Masucci MG. Remodeling of the ribosomal quality control and integrated stress response by viral ubiquitin deconjugases. Nat Commun 2023; 14:8315. [PMID: 38097648 PMCID: PMC10721647 DOI: 10.1038/s41467-023-43946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
The strategies adopted by viruses to reprogram the translation and protein quality control machinery and promote infection are poorly understood. Here, we report that the viral ubiquitin deconjugase (vDUB)-encoded in the large tegument protein of Epstein-Barr virus (EBV BPLF1)-regulates the ribosomal quality control (RQC) and integrated stress responses (ISR). The vDUB participates in protein complexes that include the RQC ubiquitin ligases ZNF598 and LTN1. Upon ribosomal stalling, the vDUB counteracts the ubiquitination of the 40 S particle and inhibits the degradation of translation-stalled polypeptides by the proteasome. Impairment of the RQC correlates with the readthrough of stall-inducing mRNAs and with activation of a GCN2-dependent ISR that redirects translation towards upstream open reading frames (uORFs)- and internal ribosome entry sites (IRES)-containing transcripts. Physiological levels of active BPLF1 promote the translation of the EBV Nuclear Antigen (EBNA)1 mRNA in productively infected cells and enhance the release of progeny virus, pointing to a pivotal role of the vDUB in the translation reprogramming that enables efficient virus production.
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Affiliation(s)
- Jiangnan Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Noemi Nagy
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Carlos Ayala-Torres
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Francisco Aguilar-Alonso
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco Morais-Esteves
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Shanshan Xu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria G Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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9
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Zhang M, Shao Y, Gu W. The Mechanism of Ubiquitination or Deubiquitination Modifications in Regulating Solid Tumor Radiosensitivity. Biomedicines 2023; 11:3240. [PMID: 38137461 PMCID: PMC10741492 DOI: 10.3390/biomedicines11123240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Radiotherapy, a treatment method employing radiation to eradicate tumor cells and subsequently reduce or eliminate tumor masses, is widely applied in the management of numerous patients with tumors. However, its therapeutic effectiveness is somewhat constrained by various drug-resistant factors. Recent studies have highlighted the ubiquitination/deubiquitination system, a reversible molecular modification pathway, for its dual role in influencing tumor behaviors. It can either promote or inhibit tumor progression, impacting tumor proliferation, migration, invasion, and associated therapeutic resistance. Consequently, delving into the potential mechanisms through which ubiquitination and deubiquitination systems modulate the response to radiotherapy in malignant tumors holds paramount significance in augmenting its efficacy. In this paper, we comprehensively examine the strides made in research and the pertinent mechanisms of ubiquitination and deubiquitination systems in governing radiotherapy resistance in tumors. This underscores the potential for developing diverse radiosensitizers targeting distinct mechanisms, with the aim of enhancing the effectiveness of radiotherapy.
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Affiliation(s)
| | - Yingjie Shao
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China;
| | - Wendong Gu
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China;
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10
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Roh J, Kim B, Im M, Jang W, Chae Y, Kang J, Youn B, Kim W. MALAT1-regulated gene expression profiling in lung cancer cell lines. BMC Cancer 2023; 23:818. [PMID: 37667226 PMCID: PMC10476395 DOI: 10.1186/s12885-023-11347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/28/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is the most common type of lung cancer and has a poor prognosis. Identifying biomarkers based on molecular mechanisms is critical for early diagnosis, timely treatment, and improved prognosis of lung cancer. MALAT1 has been reported to have overexpressed and tumor-promoting functions in NSCLC. It has been proposed as a potential biomarker for the diagnosis and prognosis of cancer. Therefore, this study was conducted to profile the changes in gene expression according to the regulation of expression of MALAT1 in NSCLC cell lines and to investigate the correlation through bioinformatic analysis of differentially expressed genes (DEGs). METHODS MALAT1 expression levels were measured using RT-qPCR. The biological functions of MALAT1 in NSCLC were analyzed by cell counting, colony forming, wound-healing, and Transwell invasion assays. In addition, gene expression profiling in response to the knockdown of MALAT1 was analyzed by transcriptome sequencing, and differentially expressed genes regulated by MALAT1 were performed by GO and KEGG pathway enrichment analyses. Bioinformatic databases were used for gene expression analysis and overall survival analysis. RESULTS Comparative analysis versus MALAT1 expression in MRC5 cells (a normal lung cell line) and the three NSCLC cell lines showed that MALAT1 expression was significantly higher in the NSCLC cells. MALAT1 knockdown decreased cell survival, proliferation, migration, and invasion in all three NSCLC cell lines. RNA-seq analysis of DEGs in NSCLC cells showed 198 DEGs were upregulated and 266 DEGs downregulated by MALAT1 knockdown in all three NSCLC cell lines. Survival analysis on these common DEGs performed using the OncoLnc database resulted in the selection of five DEGs, phosphoglycerate mutase 1 (PGAM1), phosphoglycerate mutase 4 (PGAM4), nucleolar protein 6 (NOL6), nucleosome assembly protein 1 like 5 (NAP1L5), and sestrin1 (SESN1). The gene expression levels of these selected DEGs were proved to gene expression analysis using the TNMplot database. CONCLUSION MALAT1 might function as an oncogene that enhances NSCLC cell survival, proliferation, colony formation, and invasion. RNA-seq and bioinformatic analyses resulted in the selection of five DEGs, PGAM1, PGAM4, NOL6, NAP1L5, and SESN1, which were found to be closely related to patient survival and tumorigenesis. We believe that further investigation of these five DEGs will provide valuable information on the oncogenic role of MALAT1 in NSCLC.
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Affiliation(s)
- Jungwook Roh
- Department of Science Education, Korea National University of Education, Cheongju-si, 28173, Chungbuk, Republic of Korea
| | - Boseong Kim
- Department of Science Education, Korea National University of Education, Cheongju-si, 28173, Chungbuk, Republic of Korea
| | - Mijung Im
- Department of Science Education, Korea National University of Education, Cheongju-si, 28173, Chungbuk, Republic of Korea
| | - Wonyi Jang
- Department of Science Education, Korea National University of Education, Cheongju-si, 28173, Chungbuk, Republic of Korea
| | - Yeonsoo Chae
- Department of Science Education, Korea National University of Education, Cheongju-si, 28173, Chungbuk, Republic of Korea
| | - JiHoon Kang
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - BuHyun Youn
- Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Wanyeon Kim
- Department of Science Education, Korea National University of Education, Cheongju-si, 28173, Chungbuk, Republic of Korea.
- Department of Biology Education, Korea National University of Education, Cheongju-si, 28173, Chungbuk, Republic of Korea.
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11
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Sanati M, Afshari AR, Ahmadi SS, Moallem SA, Sahebkar A. Modulation of the ubiquitin-proteasome system by phytochemicals: Therapeutic implications in malignancies with an emphasis on brain tumors. Biofactors 2023; 49:782-819. [PMID: 37162294 DOI: 10.1002/biof.1958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/20/2023] [Indexed: 05/11/2023]
Abstract
Regarding the multimechanistic nature of cancers, current chemo- or radiotherapies often fail to eradicate disease pathology, and frequent relapses or resistance to therapies occur. Brain malignancies, particularly glioblastomas, are difficult-to-treat cancers due to their highly malignant and multidimensional biology. Unfortunately, patients suffering from malignant tumors often experience poor prognoses and short survival periods. Thus far, significant efforts have been conducted to discover novel and more effective modalities. To that end, modulation of the ubiquitin-proteasome system (UPS) has attracted tremendous interest since it affects the homeostasis of proteins critically engaged in various cell functions, for example, cell metabolism, survival, proliferation, and differentiation. With their safe and multimodal actions, phytochemicals are among the promising therapeutic tools capable of turning the operation of various UPS elements. The present review, along with an updated outline of the role of UPS dysregulation in multiple cancers, provided a detailed discussion on the impact of phytochemicals on the UPS function in malignancies, especially brain tumors.
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Affiliation(s)
- Mehdi Sanati
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Birjand University of Medical Sciences, Birjand, Iran
- Experimental and Animal Study Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Amir R Afshari
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
- Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Seyed Sajad Ahmadi
- Department of Ophthalmology, Khatam-Ol-Anbia Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Adel Moallem
- Department of Pharmacology and Toxicology, College of Pharmacy, Al-Zahraa University for Women, Karbala, Iraq
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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12
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Li Y, Feng Y, Luo F, Peng G, Li Y. Positive regulators of T cell functions as predictors of prognosis and microenvironment characteristics of low-grade gliomas. Front Immunol 2023; 13:1089792. [PMID: 36726969 PMCID: PMC9885161 DOI: 10.3389/fimmu.2022.1089792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/28/2022] [Indexed: 01/17/2023] Open
Abstract
Background Low-grade gliomas (LGG) are one of the most prevalent types of brain cancers. The efficacy of immunotherapy in LGG is limited compared to other cancers. Immunosuppression in the tumor microenvironment (TME) of LGG is one of the main reasons for the low efficacy of immunotherapy. Recent studies have identified 33 positive regulators of T cell functions (TPRs) that play a critical role in promoting the proliferation, activity, and functions of multiple immunocytes. However, their role in the TME of LGG has not been investigated. This study aimed to construct a risk model based on these TPRs and to detect the significance of immunotypes in predicting LGG prognosis and immunotherapy efficacy. Methods A total of 688 LGGs and 202 normal brain tissues were extracted from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and Genotype-Tissue Expression (GTEx) databases. The NMF R package was used to identify TRP-related subtypes. The TPR prognostic model was established using the least absolute shrinkage and selection operator (LASSO) algorithm to predict the overall survival of LGG samples. Results The Subtype 2 patients had worse survival outcomes, suppressed immune function, and higher immune cell infiltration. A risk regression model consisting of 14 TPRs was established, and its performance was validated in CGGA325 cohorts. The low-risk group exhibited better overall survival, immune microenvironment, and immunotherapy response, as determined via the TIDE algorithm, indicating that increasing the level of immune infiltration can effectively improve the response to immunotherapy in the low-risk group. The risk score was determined to be an independent hazard factor (p<0.001) although other clinical features (age, sex, grade, IDH status, 1p19q codel status, MGMT status, and accepted radiotherapy) were considered. Lastly, high-risk groups in both cohorts revealed optimal drug responses to rapamycin, paclitaxel, JW-7-52-1, and bortezomib. Conclusions Our study identified two distinct TPR subtypes and built a TPR signature to elucidate the characteristics of T cell proliferation in LGG and its association with immune status and prognosis. These findings shed light on possible immunotherapeutic strategies for LGGs.
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Affiliation(s)
- Yang Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China,PET-CT Center, Chenzhou First People’s Hospital, Chenzhou, Hunan, China
| | - Yabo Feng
- PET-CT Center, Chenzhou First People’s Hospital, Chenzhou, Hunan, China
| | - Fushu Luo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Gang Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yueran Li
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Yueran Li,
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13
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Wang T, Jin C, Yang P, Chen Z, Ji J, Sun Q, Yang S, Feng Y, Tang J, Sun Y. UBE2J1 inhibits colorectal cancer progression by promoting ubiquitination and degradation of RPS3. Oncogene 2023; 42:651-664. [PMID: 36567344 PMCID: PMC9957728 DOI: 10.1038/s41388-022-02581-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022]
Abstract
Ubiquitin-conjugating enzyme E2 J1 (UBE2J1) has been proven to participate in the ubiquitination of multiple substrate proteins. However, the underlying mechanisms of UBE2J1 as a ubiquitin-conjugating enzyme participating in cancer development and progression remain largely unknown. Here, we identified that UBE2J1 is downregulated in colorectal cancer (CRC) tissues and cell lines which are mediated by DNA hypermethylation of its promoter, and decreased UBE2J1 is associated with poor prognosis. Functionally, UBE2J1 serving as a suppressor gene inhibits the proliferation and metastasis of CRC cells. Mechanistically, UBE2J1-TRIM25, forming an E2-E3 complex, physically interacts with and targets RPS3 for ubiquitination and degradation at the K214 residue. The downregulated RPS3 caused by UBE2J1 overexpression restrains NF-κB translocation into the nucleus and therefore inactivates the NF-κB signaling pathway. Our study revealed a novel role of UBE2J1-mediated RPS3 poly-ubiquitination and degradation in disrupting the NF-κB signaling pathway, which may serve as a novel and promising biomarker and therapeutic target for CRC.
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Affiliation(s)
- Tuo Wang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Chi Jin
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Peng Yang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Zhihao Chen
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Jiangzhou Ji
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Qingyang Sun
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Sheng Yang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Yifei Feng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China. .,The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China. .,The Colorectal Institute of Nanjing Medical University, Nanjing, China. .,Nanjing Medical University, Nanjing, China.
| | - Junwei Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China. .,The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China. .,The Colorectal Institute of Nanjing Medical University, Nanjing, China. .,Nanjing Medical University, Nanjing, China.
| | - Yueming Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China. .,The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China. .,The Colorectal Institute of Nanjing Medical University, Nanjing, China. .,Nanjing Medical University, Nanjing, China.
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14
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Yang Y, Yu X, Wei P, Liu C, Chen Z, Li X, Liu X. Comparative chloroplast genome and transcriptome analysis on the ancient genus Isoetes from China. FRONTIERS IN PLANT SCIENCE 2022; 13:924559. [PMID: 35968088 PMCID: PMC9372280 DOI: 10.3389/fpls.2022.924559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Isoetes is a famous living fossil that plays a significant role in the evolutionary studies of the plant kingdom. To explore the adaptive evolution of the ancient genus Isoetes from China, we focused on Isoetes yunguiensis (Q.F. Wang and W.C. Taylor), I. shangrilaensis (X. Li, Y.Q. Huang, X.K. Dai & X. Liu), I. taiwanensis (DeVol), I. sinensis (T.C. Palmer), I. hypsophila_GHC (Handel-Mazzetti), and I. hypsophila_HZS in this study. We sequenced, assembled, and annotated six individuals' chloroplast genomes and transcriptomes, and performed a series of analyses to investigate their chloroplast genome structures, RNA editing events, and adaptive evolution. The six chloroplast genomes of Isoetes exhibited a typical quadripartite structure with conserved genome sequence and structure. Comparative analyses of Isoetes species demonstrated that the gene organization, genome size, and GC contents of the chloroplast genome are highly conserved across the genus. Besides, our positive selection analyses suggested that one positively selected gene was statistically supported in Isoetes chloroplast genomes using the likelihood ratio test (LRT) based on branch-site models. Moreover, we detected positive selection signals using transcriptome data, suggesting that nuclear-encoded genes involved in the adaption of Isoetes species to the extreme environment of the Qinghai-Tibetan Plateau (QTP). In addition, we identified 291-579 RNA editing sites in the chloroplast genomes of six Isoetes based on transcriptome data, well above the average of angiosperms. RNA editing in protein-coding transcripts results from amino acid changes to increase their hydrophobicity and conservation in Isoetes, which may help proteins form functional three-dimensional structure. Overall, the results of this study provide comprehensive transcriptome and chloroplast genome resources and contribute to a better understanding of adaptive evolutionary and molecular biology in Isoetes.
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Affiliation(s)
- Yujiao Yang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaolei Yu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhuyifu Chen
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan, China
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, China
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15
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Elhamamsy AR, Metge BJ, Alsheikh HA, Shevde LA, Samant RS. Ribosome Biogenesis: A Central Player in Cancer Metastasis and Therapeutic Resistance. Cancer Res 2022; 82:2344-2353. [PMID: 35303060 PMCID: PMC9256764 DOI: 10.1158/0008-5472.can-21-4087] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 01/07/2023]
Abstract
Ribosomes are a complex ensemble of rRNA and ribosomal proteins that function as mRNA translation machines. Ribosome biogenesis is a multistep process that begins in the nucleolus and concludes in the cytoplasm. The process is tightly controlled by multiple checkpoint and surveillance pathways. Perturbations in these checkpoints and pathways can lead to hyperactivation of ribosome biogenesis. Emerging evidence suggests that cancer cells harbor a specialized class of ribosomes (onco-ribosomes) that facilitates the oncogenic translation program, modulates cellular functions, and promotes metabolic rewiring. Mutations in ribosomal proteins, rRNA processing, and ribosome assembly factors result in ribosomopathies that are associated with an increased risk of developing malignancies. Recent studies have linked mutations in ribosomal proteins and aberrant ribosomes with poor prognosis, highlighting ribosome-targeted therapy as a promising approach for treating patients with cancer. Here, we summarize various aspects of dysregulation of ribosome biogenesis and the impact of resultant onco-ribosomes on malignant tumor behavior, therapeutic resistance, and clinical outcome. Ribosome biogenesis is a promising therapeutic target, and understanding the important determinants of this process will allow for improved and perhaps selective therapeutic strategies to target ribosome biosynthesis.
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Affiliation(s)
- Amr R. Elhamamsy
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Brandon J. Metge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Heba A. Alsheikh
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lalita A. Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rajeev S. Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.,Birmingham VA Medical Center, Birmingham, Alabama.,Corresponding Author: Rajeev S. Samant, The University of Alabama at Birmingham, WTI 320E, 1824 6th Avenue South, Birmingham, AL 35233. Phone: 205-975-6262; E-mail:
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16
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Rui X, Huang Z, Chen R, Chen Y, Wang Y, Huang Z. RPS3 Promotes the Metastasis and Cisplatin Resistance of Adenoid Cystic Carcinoma. Front Oncol 2022; 12:804439. [PMID: 35847905 PMCID: PMC9280127 DOI: 10.3389/fonc.2022.804439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
Background Adenoid cystic carcinoma (ACC) is a malignant tumor in salivary gland tissue, that is characterized by strong invasiveness and lung metastasis, leading to poor survival rates. RPS3 is been reported to be associated with the biological functions of tumor cells. This study explored the regulatory effect of RPS3 in ACC to provide new therapeutic targets for ACC therapy. Methods We reviewed the clinical and pathologic data of 73 ACC patients. The expression of RPS3 was examined in ACC by immunohistochemistry. Transwell, wound healing, half-maximal inhibitory concentration (IC50) and other experiments were used to determine the regulatory effect of RPS3 on ACC functions. Coimmunoprecipitation and mass spectrometry analysis were used to detect the binding proteins of RPS3, mechanisms by which RPS3/STAT1/NF-kB signaling regulates ACC behavior were assessed using western blotting (WB), qPCR, etc. To explore the regulatory effect of RPS3 on ACC in vivo, we constructed nude mouse sciatic nerve infiltration model and a lung metastasis model for studies. Results High RPS3 expression was associated with metastasis and a poor prognosis in ACC patients. Inhibition of RPS3 expression reduced ACC migration, invasion and cisplatin resistance, and overexpression of RPS3 promoted ACC migration, invasion and cisplatin resistance. Further experiments revealed that RPS3 can activate the STAT1/NF-kB signaling pathway and regulate ACC behavior through binding to STAT1. The incidence of sciatic nerve infiltration and lung metastasis in nude mice after RPS3 knockdown was lower than that of the control group in vivo. Conclusion RPS3 is highly expressed and associated with the prognosis and survival of ACC patients. The RPS3/STAT1/NF-kB pathway may play an important regulatory role in ACC migration, invasion and chemoresistance. As a new therapeutic target of ACC, its clinical application value is worthy of attention and further exploration.
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Affiliation(s)
- Xi Rui
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zixian Huang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Chen
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yongju Chen
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Wang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Zhiquan Huang, ; ; Yan Wang,
| | - Zhiquan Huang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Zhiquan Huang, ; ; Yan Wang,
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17
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Lu Y, Huang R, Ying J, Li X, Jiao T, Guo L, Zhou H, Wang H, Tuersuntuoheti A, Liu J, Chen Q, Wang Y, Su L, Guo C, Xu F, Wang Z, Lu Y, Li K, Liang J, Huang Z, Chen X, Yao J, Hu H, Cheng X, Wan Y, Chen X, Zhang N, Miao S, Cai J, Wang L, Liu C, Song W, Zhao H. RING finger 138 deregulation distorts NF-кB signaling and facilities colitis switch to aggressive malignancy. Signal Transduct Target Ther 2022; 7:185. [PMID: 35697692 PMCID: PMC9192753 DOI: 10.1038/s41392-022-00985-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
Abstract
Prolonged activation of nuclear factor (NF)-кB signaling significantly contributes to the development of colorectal cancer (CRC). New therapeutic opportunities are emerging from targeting this distorted cell signaling transduction. Here, we discovered the critical role of RING finger 138 (RNF138) in CRC tumorigenesis through regulating the NF-кB signaling, which is independent of its Ubiquitin-E3 ligase activity involved in DNA damage response. RNF138−/− mice were hyper-susceptible to the switch from colitis to aggressive malignancy, which coincided with sustained aberrant NF-кB signaling in the colonic cells. Furthermore, RNF138 suppresses the activation of NF-кB signaling pathway through preventing the translocation of NIK and IKK-Beta Binding Protein (NIBP) to the cytoplasm, which requires the ubiquitin interaction motif (UIM) domain. More importantly, we uncovered a significant correlation between poor prognosis and the downregulation of RNF138 associated with reinforced NF-кB signaling in clinical settings, raising the possibility of RNF138 dysregulation as an indicator for the therapeutic intervention targeting NF-кB signaling. Using the xenograft models built upon either RNF138-dificient CRC cells or the cells derived from the RNF138-dysregulated CRC patients, we demonstrated that the inhibition of NF-кB signaling effectively hampered tumor growth. Overall, our work defined the pathogenic role of aberrant NF-кB signaling due to RNF138 downregulation in the cascade events from the colitis switch to colonic neoplastic transformation and progression, and also highlights the possibility of targeting the NF-кB signaling in treating specific subtypes of CRC indicated by RNF138-ablation.
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Affiliation(s)
- Yalan Lu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.,Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, 100021, China
| | - Rong Huang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.,National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Jianming Ying
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xingchen Li
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tao Jiao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Lei Guo
- Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Haitao Zhou
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Han Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Amannisa Tuersuntuoheti
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Jianmei Liu
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qichen Chen
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yanhong Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Luying Su
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Changyuan Guo
- Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fu Xu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Ziyi Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yan Lu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Kai Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Junbo Liang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Zhen Huang
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiao Chen
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jinjie Yao
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hanjie Hu
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaowen Cheng
- Department of Clinical Laboratory, the First Affiliated Hospital, Anhui Medical University, Hefei, 230022, China
| | - Yufeng Wan
- Department of Clinical Laboratory, the First Affiliated Hospital, Anhui Medical University, Hefei, 230022, China
| | - Xinyan Chen
- Department of Clinical Laboratory, the First Affiliated Hospital, Anhui Medical University, Hefei, 230022, China
| | - Ning Zhang
- Wellcome Centre for Anti-Infectives Research (WCAIR), Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Shiying Miao
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Linfang Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Changzheng Liu
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
| | - Hong Zhao
- Department of Hepatobiliary Surgery, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China. .,Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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18
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Chen F, Wang N, He X. Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance. Front Aging Neurosci 2022; 14:884367. [PMID: 35615586 PMCID: PMC9125150 DOI: 10.3389/fnagi.2022.884367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Background Alzheimer's disease (AD) is a common neurodegenerative disease. The pathogenesis is complex and has not been clearly elucidated, and there is no effective treatment. Recent studies have demonstrated that DNA methylation is closely associated with the pathogenesis of AD, which sheds light on investigating potential biomarkers for the diagnosis of early AD and related possible therapeutic approaches. Methods Alzheimer's disease patients samples and healthy controls samples were collected from two datasets in the GEO database. Using LIMMA software package in R language to find differentially expressed genes (DEGs). Afterward, DEGs have been subjected to enrichment analysis of GO and KEGG pathways. The PPI networks and Hub genes were created and visualized based on the STRING database and Cytoscape. ROC curves were further constructed to analyze the accuracy of these genes for AD diagnosis. Results Analysis of the GSE109887 and GSE97760 datasets showed 477 significant DEGs. GO and KEGG enrichment analysis showed terms related to biological processes related to these genes. The top ten Hub genes were found on the basis of the PPI network using the CytoHubba plugin, and the AUC areas of these top ranked genes were all greater than 0.7, showing satisfactory diagnostic accuracy. Conclusion The study identified the top 10 Hub genes associated with AD-related DNA methylation, of which RPSA, RPS23, and RPLP0 have high diagnostic accuracy and excellent AD biomarker potential.
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Affiliation(s)
| | | | - Xiaping He
- School of Basic Medical Sciences, Dali University, Dali, China
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19
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Dong J, He J, Zhang Z, Zhang W, Li Y, Li D, Xie H, Zuo W, Tang J, Zeng Z, Cai W, Lai L, Yun M, Shen L, Yin L, Tang D, Dai Y. Identification of lysine acetylome of oral squamous cell carcinoma by label-free quantitative proteomics. J Proteomics 2022; 262:104598. [PMID: 35489685 DOI: 10.1016/j.jprot.2022.104598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
Abstract
Lysine acetylation (Kac) on histone promotes relaxation of the chromatin conformation and favors gene transcription to regulate oncogenesis, whereas the total acetylation profiling of oral squamous cell carcinoma (OSCC) is unknown. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was utilised to investigate lysine acetylation features of tumor tissues and adjacent normal tissues from 9 patients with OCSS. 282 upregulated Kac sites in 234 proteins and 235 downregulated Kac sites in 162 proteins between OSCC tissues and paired adjacent normal tissues were identified. Different acetylation proteins (DAPs) were analyzed through KEGG-based and MCODE. These DAPs are enriched in the ribosome biogenesis pathway. Survival Analysis of hub genes with TCGA database was performed. In addition, IPA software was used to explore the connection between 9 core DAPs (RPS3, RPL24, RPL19, EIF4A2, RPL12, MYBPC1, RPS6, ARCN1, and TMEM9) and the different expression of KATs and KDACs identified in our proteomic. The study is the first comparative study of Kac modification on oral squamous cell carcinoma. We propose to put forward the hypothesis that the dysfunction of ribosome biogenesis caused by the change of Lysine acetylation, especially downregulated acetylation on RPS6 and RPS3 may associated with the pathogenesis of OSCC. SIGNIFICANCE: The study is the first comparative study of Kac modification on oral squamous cell carcinoma through LC-MS/MS-based modified proteomic. These DAPs are high enriched in the ribosome biogenesis pathway. Used MCODE and survival analysis, 9 core DAPs (RPS3, RPL24, RPL19, EIF4A2, RPL12, MYBPC1, RPS6, ARCN1, and TMEM9) were screened. IPA software was used to explore the connection between 9 core DAPs and the different expression of KATs and KDACs identified in our proteomic. In addition, we propose to put forward the hypothesis that the dysfunction of ribosome biogenesis caused by the change of Lysine acetylation, especially downregulated acetylation on RPS6 and RPS3 may associated with the pathogenesis of OSCC.
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Affiliation(s)
- Jingjing Dong
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China; Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Jingquan He
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Zeyu Zhang
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Wei Zhang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Yixi Li
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Dandan Li
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Hongliang Xie
- Stomatology Department, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Wenxin Zuo
- Stomatology Department, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Jianming Tang
- Stomatology Department, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Zhipeng Zeng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Wanxia Cai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China
| | - Liusheng Lai
- Guangxi Key Laboratory of Metabolic Diseases Research, Affiliated No. 924 Hospital, Southern Medical University, Guilin 541002, Guangxi, China
| | - Manhua Yun
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Lingjun Shen
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Lianghong Yin
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China.
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China.
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, Guangdong 518020, PR China; Guangxi Key Laboratory of Metabolic Diseases Research, Affiliated No. 924 Hospital, Southern Medical University, Guilin 541002, Guangxi, China.
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20
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Huang L, Xu W, Liu H, Xue M, Liu X, Zhang K, Hu L, Li J, Liu X, Xiang Z, Zheng J, Li C, Chen W, Bu Z, Xiong T, Weng C. African Swine Fever Virus pI215L Negatively Regulates cGAS-STING Signaling Pathway through Recruiting RNF138 to Inhibit K63-Linked Ubiquitination of TBK1. THE JOURNAL OF IMMUNOLOGY 2021; 207:2754-2769. [PMID: 34759016 DOI: 10.4049/jimmunol.2100320] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/17/2021] [Indexed: 11/19/2022]
Abstract
African swine fever is a severe animal infectious disease caused by African swine fever virus (ASFV), and the morbidity and mortality associated with virulent ASFV isolates are as high as 100%. Previous studies showed that the ability of ASFV to antagonize IFN production is closely related to its pathogenicity. Here, we report that ASFV HLJ/18 infection induced low levels of type I IFN and inhibited cGMP-AMP-induced type I IFN production in porcine alveolar macrophages that were isolated from specific pathogen-free Landrace piglets. Subsequently, an unbiased screen was performed to screen the ASFV genes with inhibitory effects on the type I IFN production. ASFV pI215L, a viral E2 ubiquitin-conjugating enzyme, was identified as one of the strongest inhibitory effectors on the production of type I IFN. Knockdown of pI215L expression inhibited ASFV replication and enhanced IFN-β production. However, inhibition of type I IFN production by pI215L was independent of its E2 enzyme activity. Furthermore, we found that pI215L inhibited type I IFN production and K63-linked polyubiquitination of TANK-binding kinase 1 through pI215L-binding RING finger protein 138 (RNF138). ASFV pI215L enhanced the interaction between RNF138 and RNF128 and promoted RNF138 to degrade RNF128, which resulted in reduced K63-linked polyubiquitination of TANK-binding kinase 1 and type І IFN production. Taken together, our findings reveal a novel immune escape mechanism of ASFV, which provides a clue to the design and development of an immune-sensitive attenuated live vaccine.
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Affiliation(s)
- Li Huang
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Wenjie Xu
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and.,College of Life Sciences, Yangtze University, Jingzhou 434025, China
| | - Hongyang Liu
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Mengdi Xue
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Xiaohong Liu
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Kunli Zhang
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Liang Hu
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Jiangnan Li
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Xuemin Liu
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Zhida Xiang
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and.,College of Life Sciences, Yangtze University, Jingzhou 434025, China
| | - Jun Zheng
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Changyao Li
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Weiye Chen
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Zhigao Bu
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and
| | - Tao Xiong
- College of Life Sciences, Yangtze University, Jingzhou 434025, China
| | - Changjiang Weng
- Division of Fundamental Immunology, National African Swine Fever Para-reference Laboratory, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; and .,College of Life Sciences, Yangtze University, Jingzhou 434025, China
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21
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Chen TW, Chang KP, Cheng CC, Chen CY, Hong SW, Sie ZL, Cheng HW, Yen WC, Huang Y, Liu SC, Wang CI. Characterization of Recurrent Relevant Genes Reveals a Novel Role of RPL36A in Radioresistant Oral Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13225623. [PMID: 34830778 PMCID: PMC8616119 DOI: 10.3390/cancers13225623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/31/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Radioresistance is one of the major factors contributing to radiotherapy failure in OSCC. By systematically comparing the prognostic values of all genes in TCGA-OSCC patients with and without radiotherapy, radioresistance-associated genes were identified. Higher RPL36A transcript levels were found to be associated with a poor prognosis only in OSCC patients with radiotherapy in the cohort of TCGA and another independent Taiwanese cohort. RPL36A was then shown to be involved in the regulation of DNA damage, cell cycle and apoptosis, leading to radioresistance. Thus, such integrated studies are expected to be greatly beneficial for the development of new therapeutic interventions for radioresistant OSCC in the future. Abstract Radioresistance is one of the major factors that contributes to radiotherapy failure in oral cavity squamous cell carcinoma (OSCC). By comparing the prognostic values of 20,502 genes expressed in patients in The Cancer Genome Atlas (TCGA)-OSCC cohort with (n = 162) and without radiotherapy (n = 118), herein identified 297 genes positively correlated with poor disease-free survival in OSCC patients with radiotherapy as the potential radioresistance-associated genes. Among the potential radioresistance-associated genes, 36 genes were upregulated in cancerous tissues relative to normal tissues. The bioinformatics analysis revealed that 60S ribosomal protein L36a (RPL36A) was the most frequently detected gene involved in radioresistance-associated gene-mediated biological pathways. Then, two independent cohorts (n = 162 and n = 136) were assessed to confirm that higher RPL36A transcript levels were significantly associated with a poor prognosis only in OSCC patients with radiotherapy. Mechanistically, we found that knockdown of RPL36A increased radiosensitivity via sensitizing cells to DNA damage and promoted G2/M cell cycle arrest followed by augmenting the irradiation-induced apoptosis pathway in OSCC cells. Taken together, our study supports the use of large-scale genomic data for identifying specific radioresistance-associated genes and suggests a regulatory role for RPL36A in the development of radioresistance in OSCC.
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Affiliation(s)
- Ting-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan;
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Kai-Ping Chang
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (K.-P.C.); (H.-W.C.); (W.-C.Y.)
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
| | - Chun-Chia Cheng
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University, Taoyuan 333, Taiwan; (C.-C.C.); (S.-W.H.); (Z.-L.S.)
| | - Cheng-Yi Chen
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
| | - Shu-Wen Hong
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University, Taoyuan 333, Taiwan; (C.-C.C.); (S.-W.H.); (Z.-L.S.)
| | - Zong-Lin Sie
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University, Taoyuan 333, Taiwan; (C.-C.C.); (S.-W.H.); (Z.-L.S.)
| | - Hsing-Wen Cheng
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (K.-P.C.); (H.-W.C.); (W.-C.Y.)
| | - Wei-Chen Yen
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (K.-P.C.); (H.-W.C.); (W.-C.Y.)
| | - Yenlin Huang
- Department of Pathology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
| | - Shu-Chen Liu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan 333, Taiwan
- Correspondence: (S.-C.L.); (C.-I.W.); Tel.: +886-3-4227151 (ext. 27754) (S.-C.L.); +886-3-2118800 (ext. 3032) (C.-I.W.)
| | - Chun-I Wang
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University, Taoyuan 333, Taiwan; (C.-C.C.); (S.-W.H.); (Z.-L.S.)
- Correspondence: (S.-C.L.); (C.-I.W.); Tel.: +886-3-4227151 (ext. 27754) (S.-C.L.); +886-3-2118800 (ext. 3032) (C.-I.W.)
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Kang H, Lee S, Kim K, Jeon J, Kang SG, Youn H, Kim HY, Youn B. Downregulated CLIP3 induces radioresistance by enhancing stemness and glycolytic flux in glioblastoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:282. [PMID: 34488821 PMCID: PMC8420000 DOI: 10.1186/s13046-021-02077-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022]
Abstract
Background Glioblastoma Multiforme (GBM) is a malignant primary brain tumor in which the standard treatment, ionizing radiation (IR), achieves a median survival of about 15 months. GBM harbors glioblastoma stem-like cells (GSCs), which play a crucial role in therapeutic resistance and recurrence. Methods Patient-derived GSCs, GBM cell lines, intracranial GBM xenografts, and GBM sections were used to measure mRNA and protein expression and determine the related molecular mechanisms by qRT-PCR, immunoblot, immunoprecipitation, immunofluorescence, OCR, ECAR, live-cell imaging, and immunohistochemistry. Orthotopic GBM xenograft models were applied to investigate tumor inhibitory effects of glimepiride combined with radiotherapy. Results We report that GSCs that survive standard treatment radiation upregulate Speedy/RINGO cell cycle regulator family member A (Spy1) and downregulate CAP-Gly domain containing linker protein 3 (CLIP3, also known as CLIPR-59). We discovered that Spy1 activation and CLIP3 inhibition coordinately shift GBM cell glucose metabolism to favor glycolysis via two cellular processes: transcriptional regulation of CLIP3 and facilitating Glucose transporter 3 (GLUT3) trafficking to cellular membranes in GBM cells. Importantly, in combination with IR, glimepiride, an FDA-approved medication used to treat type 2 diabetes mellitus, disrupts GSCs maintenance and suppresses glycolytic activity by restoring CLIP3 function. In addition, combining radiotherapy and glimepiride significantly reduced GBM growth and improved survival in a GBM orthotopic xenograft mouse model. Conclusions Our data suggest that radioresistant GBM cells exhibit enhanced stemness and glycolytic activity mediated by the Spy1-CLIP3 axis. Thus, glimepiride could be an attractive strategy for overcoming radioresistance and recurrence by rescuing CLIP3 expression. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02077-4.
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Affiliation(s)
- Hyunkoo Kang
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Sungmin Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea.,Present address: Institute of Bioinnovation Research, Kolon Life Science, Seoul, Republic of Korea
| | - Kyeongmin Kim
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Jaewan Jeon
- Department of Radiation Oncology, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Seok-Gu Kang
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Medical Sciences, Yonsei University Graduate School, Seoul, Republic of Korea
| | - HyeSook Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, Republic of Korea
| | - Hae Yu Kim
- Department of Neurosurgery, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - BuHyun Youn
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea. .,Department of Biological Sciences, Pusan National University, Busandaehak-ro 63beon-gil 2, Geumjeong-gu, Busan, 46241, Republic of Korea.
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23
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Seo D, Roh J, Chae Y, Kim W. Gene expression profiling after LINC00472 overexpression in an NSCLC cell line. Cancer Biomark 2021; 32:175-188. [PMID: 34397405 DOI: 10.3233/cbm-210242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lung cancer accounts for a large proportion of cancer-related deaths worldwide. Personalized therapeutic medicine based on the genetic characteristics of non-small cell lung cancer (NSCLC) is a promising field, and discovering clinically applicable biomarkers of NSCLC is required. LINC00472 is a long non-coding RNA and has been recently suggested to be a biomarker of NSCLC, but little is known of its mechanism in NSCLC. Thus, the current study was performed to document changes in gene expression after LINC00472 overexpression in NSCLC cells. As a result of cell viability and migration assay, LINC00472 downregulated cell survival, proliferation, and motility. Transcriptome sequencing analysis showed 3,782 genes expression were changed in LINC00472 overexpressing cells. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed most genes were associated with intracellular metabolism. The PPP1R12B, RGS5, RBM5, RBL2, LDLR and PTPRM genes were upregulated by LINC00472 overexpression and these genes functioned as tumor suppressors in several cancers. In contrast, SPSB1, PCNA, CD24, CDK5, CDC25A, and EIF4EBP1 were downregulated by LINC00472, and they functioned as oncogenes in various cancers. Consequently, the function of LINC00472 in tumorigenesis might be related to changes in the expressions of other oncogenes and tumor suppressors.
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Affiliation(s)
- Danbi Seo
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Jungwook Roh
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Yeonsoo Chae
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Wanyeon Kim
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Biology Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
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24
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Garzia A, Meyer C, Tuschl T. The E3 ubiquitin ligase RNF10 modifies 40S ribosomal subunits of ribosomes compromised in translation. Cell Rep 2021; 36:109468. [PMID: 34348161 DOI: 10.1016/j.celrep.2021.109468] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/02/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022] Open
Abstract
Reversible monoubiquitination of small subunit ribosomal proteins RPS2/uS5 and RPS3/uS3 has been noted to occur on ribosomes involved in ZNF598-dependent mRNA surveillance. Subsequent deubiquitination of RPS2 and RPS3 by USP10 is critical for recycling of stalled ribosomes in a process known as ribosome-associated quality control. Here, we identify and characterize the RPS2- and RPS3-specific E3 ligase Really Interesting New Gene (RING) finger protein 10 (RNF10) and its role in translation. Overexpression of RNF10 increases 40S ribosomal subunit degradation similarly to the knockout of USP10. Although a substantial fraction of RNF10-mediated RPS2 and RPS3 monoubiquitination results from ZNF598-dependent sensing of collided ribosomes, ZNF598-independent impairment of translation initiation and elongation also contributes to RPS2 and RPS3 monoubiquitination. RNF10 photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) identifies crosslinked mRNAs, tRNAs, and 18S rRNAs, indicating recruitment of RNF10 to ribosomes stalled in translation. These impeded ribosomes are tagged by ubiquitin at their 40S subunit for subsequent programmed degradation unless rescued by USP10.
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Affiliation(s)
- Aitor Garzia
- Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Cindy Meyer
- Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, Box 186, New York, NY 10065, USA.
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25
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Enhancement of Radio-Thermo-Sensitivity of 5-Iodo-2-Deoxyuridine-Loaded Polymeric-Coated Magnetic Nanoparticles Triggers Apoptosis in U87MG Human Glioblastoma Cancer Cell Line. Cell Mol Bioeng 2021; 14:365-377. [PMID: 34295445 DOI: 10.1007/s12195-021-00675-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/05/2021] [Indexed: 01/22/2023] Open
Abstract
Introduction With an emphasis on the radioresistant nature of glioblastoma cells, the aim of the present study was to evaluate the radio-thermo-sensitizing effects of PCL-PEG-coated Superparamagnetic iron oxide nanoparticles (SPIONs) as a carrier of 5-iodo-2-deoxyuridine (IUdR) in monolayer culture of U87MG human glioma cell line. Methods Following monolayer culture of U87MG cells, nanoparticle uptake was assessed using Prussian blue staining and ICP-OES method. The U87MG cells were treated with an appropriate concentration of free IUdR and PCL-PEG-coated SPIONs (MNPs) loaded with IUdR (IUdR/MNPs) for 24 h, subjected to hyperthermia (water bath and alternating magnetic field (AMF)) at 43 °C, and exposed to X-ray (2 Gy, 6 MV). The combined effects of hyperthermia with or without magnetic nanoparticles on radiosensitivity of the U87MG cells were evaluated using colony formation assay (CFA) and Flowcytometry. Results Prussian blue staining and ICP-OES showed that the nanoparticles were able to enter the cells. The results also indicated that IUdR/MNPs combined with X-ray radiation and hyperthermia significantly decreased the colony formation ability of monolayer cells (1.11, 1.41 fold) and increased the percentage of apoptotic (2.47, 4.1 fold) and necrotic cells (12.28, 29.34 fold), when compared to IUdR combined with X-ray and hyperthermia or IUdR/MNPs + X-ray. MTT results revealed that the presence of IUdR/MNPs significantly increased the toxicity of AMF hyperthermia compared to the water bath method. Conclusions Our study showed that SPIONs/PCL-PEG, as a carrier of IUdR, can enhance the cytotoxic effects of radiotherapy and hyperthermia and act as a radio-thermo-sensitizing agent. Graphic Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12195-021-00675-y.
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26
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Arya KR, Bharath Chand RP, Abhinand CS, Nair AS, Oommen OV, Sudhakaran PR. Identification of Hub Genes and Key Pathways Associated with Anti- VEGF Resistant Glioblastoma Using Gene Expression Data Analysis. Biomolecules 2021; 11:biom11030403. [PMID: 33803224 PMCID: PMC8000064 DOI: 10.3390/biom11030403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
Anti-VEGF therapy is considered to be a useful therapeutic approach in many tumors, but the low efficacy and drug resistance limit its therapeutic potential and promote tumor growth through alternative mechanisms. We reanalyzed the gene expression data of xenografts of tumors of bevacizumab-resistant glioblastoma multiforme (GBM) patients, using bioinformatics tools, to understand the molecular mechanisms of this resistance. An analysis of the gene set data from three generations of xenografts, identified as 646, 873 and 1220, differentially expressed genes (DEGs) in the first, fourth and ninth generations, respectively, of the anti-VEGF-resistant GBM cells. Gene Ontology (GO) and pathway enrichment analyses demonstrated that the DEGs were significantly enriched in biological processes such as angiogenesis, cell proliferation, cell migration, and apoptosis. The protein–protein interaction network and module analysis revealed 21 hub genes, which were enriched in cancer pathways, the cell cycle, the HIF1 signaling pathway, and microRNAs in cancer. The VEGF pathway analysis revealed nine upregulated (IL6, EGFR, VEGFA, SRC, CXCL8, PTGS2, IDH1, APP, and SQSTM1) and five downregulated hub genes (POLR2H, RPS3, UBA52, CCNB1, and UBE2C) linked with several of the VEGF signaling pathway components. The survival analysis showed that three upregulated hub genes (CXCL8, VEGFA, and IDH1) were associated with poor survival. The results predict that these hub genes associated with the GBM resistance to bevacizumab may be potential therapeutic targets or can be biomarkers of the anti-VEGF resistance of GBM.
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27
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Poonaki E, Ariakia F, Jalili-Nik M, Shafiee Ardestani M, Tondro G, Samini F, Ghasemi S, Sahab-Negah S, Gorji A. Targeting BMI-1 with PLGA–PEG nanoparticle-containing PTC209 modulates the behavior of human glioblastoma stem cells and cancer cells. Cancer Nanotechnol 2021. [DOI: 10.1186/s12645-021-00078-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AbstractDespite advances in glioblastoma (GBM) treatments, current approaches have failed to improve the overall survival of patients. The oncogene BMI-1, a core member of the polycomb group proteins, is a potential novel therapeutic target for GBM. To enhance the efficacy and reduce the toxicity, PTC209, a BMI-1 inhibitor, was loaded into a PLGA–PEG nanoparticle conjugated with CD133 antibody (Nano-PTC209) and its effect on the behavior of human GBM stem-like cells (GSCs) and the human glioblastoma cell line (U87MG) was assessed. Nano-PTC209 has a diameter of ~ 75 nm with efficient drug loading and controlled release. The IC50 values of Nano-PTC209 for GSCs and U87MG cells were considerably lower than PTC209. Nano-PTC209 significantly decreased the viability of both GSCs and U87MG cells in a dose-dependent manner and caused a significant enhancement of apoptosis and p53 levels as well as inhibition of AKT and JNK signaling pathways. Furthermore, Nano-PTC209 significantly inhibited the migration ability, decreased the activity of metalloproteinase-2 and -9, and increased the generation of reactive oxygen species in both GSCs and U87MG cells. Our data indicate that PLGA–PEG nanoparticle conjugated with CD133 antibody could be an ideal nanocarrier to deliver PTC209 and effectively target BMI-1 for potential approaches in the treatment of GBM.
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The role of E3 ubiquitin ligases in the development and progression of glioblastoma. Cell Death Differ 2021; 28:522-537. [PMID: 33432111 PMCID: PMC7862665 DOI: 10.1038/s41418-020-00696-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 12/15/2022] Open
Abstract
Despite recent advances in our understanding of the disease, glioblastoma (GB) continues to have limited treatment options and carries a dismal prognosis for patients. Efforts to stratify this heterogeneous malignancy using molecular classifiers identified frequent alterations in targetable proteins belonging to several pathways including the receptor tyrosine kinase (RTK) and mitogen-activated protein kinase (MAPK) signalling pathways. However, these findings have failed to improve clinical outcomes for patients. In almost all cases, GB becomes refractory to standard-of-care therapy, and recent evidence suggests that disease recurrence may be associated with a subpopulation of cells known as glioma stem cells (GSCs). Therefore, there remains a significant unmet need for novel therapeutic strategies. E3 ubiquitin ligases are a family of >700 proteins that conjugate ubiquitin to target proteins, resulting in an array of cellular responses, including DNA repair, pro-survival signalling and protein degradation. Ubiquitin modifications on target proteins are diverse, ranging from mono-ubiquitination through to the formation of polyubiquitin chains and mixed chains. The specificity in substrate tagging and chain elongation is dictated by E3 ubiquitin ligases, which have essential regulatory roles in multiple aspects of brain cancer pathogenesis. In this review, we begin by briefly summarising the histological and molecular classification of GB. We comprehensively describe the roles of E3 ubiquitin ligases in RTK and MAPK, as well as other, commonly altered, oncogenic and tumour suppressive signalling pathways in GB. We also describe the role of E3 ligases in maintaining glioma stem cell populations and their function in promoting resistance to ionizing radiation (IR) and chemotherapy. Finally, we consider how our knowledge of E3 ligase biology may be used for future therapeutic interventions in GB, including the use of blood-brain barrier permeable proteolysis targeting chimeras (PROTACs).
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Scholz N, Kurian KM, Siebzehnrubl FA, Licchesi JDF. Targeting the Ubiquitin System in Glioblastoma. Front Oncol 2020; 10:574011. [PMID: 33324551 PMCID: PMC7724090 DOI: 10.3389/fonc.2020.574011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma is the most common primary brain tumor in adults with poor overall outcome and 5-year survival of less than 5%. Treatment has not changed much in the last decade or so, with surgical resection and radio/chemotherapy being the main options. Glioblastoma is highly heterogeneous and frequently becomes treatment-resistant due to the ability of glioblastoma cells to adopt stem cell states facilitating tumor recurrence. Therefore, there is an urgent need for novel therapeutic strategies. The ubiquitin system, in particular E3 ubiquitin ligases and deubiquitinating enzymes, have emerged as a promising source of novel drug targets. In addition to conventional small molecule drug discovery approaches aimed at modulating enzyme activity, several new and exciting strategies are also being explored. Among these, PROteolysis TArgeting Chimeras (PROTACs) aim to harness the endogenous protein turnover machinery to direct therapeutically relevant targets, including previously considered "undruggable" ones, for proteasomal degradation. PROTAC and other strategies targeting the ubiquitin proteasome system offer new therapeutic avenues which will expand the drug development toolboxes for glioblastoma. This review will provide a comprehensive overview of E3 ubiquitin ligases and deubiquitinating enzymes in the context of glioblastoma and their involvement in core signaling pathways including EGFR, TGF-β, p53 and stemness-related pathways. Finally, we offer new insights into how these ubiquitin-dependent mechanisms could be exploited therapeutically for glioblastoma.
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Affiliation(s)
- Nico Scholz
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Kathreena M. Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, United Kingdom
| | - Florian A. Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
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30
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Graifer D, Karpova G. Ribosomal protein uS3 in cell biology and human disease: Latest insights and prospects. Bioessays 2020; 42:e2000124. [PMID: 33179285 DOI: 10.1002/bies.202000124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/14/2020] [Indexed: 12/20/2022]
Abstract
The conserved ribosomal protein uS3 in eukaryotes has long been known as one of the essential components of the small (40S) ribosomal subunit, which is involved in the structure of the 40S mRNA entry pore, ensuring the functioning of the 40S subunit during translation initiation. Besides, uS3, being outside the ribosome, is engaged in various cellular processes related to DNA repair, NF-kB signaling pathway and regulation of apoptosis. This review is devoted to recent data opening new horizons in understanding the roles of uS3 in such processes as the assembly and maturation of 40S subunits, ensuring proper structure of 48S pre-initiation complexes, regulation of initiation and ribosome-based RNA quality control pathways. Besides, we summarize novel results on the participation of the protein in processes beyond translation and consider biomedical implications of previously known and recently found extra-ribosomal functions of uS3, primarily, in oncogenesis.
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Affiliation(s)
- Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Galina Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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31
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Alam E, Maaliki L, Nasr Z. Ribosomal protein S3 selectively affects colon cancer growth by modulating the levels of p53 and lactate dehydrogenase. Mol Biol Rep 2020; 47:6083-6090. [PMID: 32748020 DOI: 10.1007/s11033-020-05683-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/26/2020] [Indexed: 01/10/2023]
Abstract
Ribosomal protein S3 (RPS3) is a component of the 40S ribosomal subunit. It is known to function in ribosome biogenesis and as an endonuclease. RPS3 has been shown to be over expressed in colon adenocarcinoma but its role in colon cancer is still unknown. In this study, we aim at determining the expression levels of RPS3 in a colon cancer cell line Caco-2 compared to a normal colon mucosa cell line NCM-460 and study the effects of targeting this protein by siRNA on cellular behavior. RPS3 was found to be expressed in both cell lines. However, siRNA treatment showed a more protruding effect on Caco-2 cells compared to NCM-460 cells. RPS3 knockdown led to a significant decrease in the proliferation, survival, migration and invasion and an increase in the apoptosis of Caco-2 cells. Western blot analysis demonstrated that these effects correlated with an increase in the level of the tumor suppressor p53 and a decrease in the level and activity of lactate dehydrogenase (LDH), an enzyme involved in the metabolism of cancer cells. No significant effect was shown in normal colon NCM-460 cells. Targeting p53 by siRNA did not affect RPS3 levels indicating that p53 may be a downstream target of RPS3. However, the concurrent knockdown of RPS3 and p53 showed no change in LDH level in Caco-2 cells suggesting an interesting interplay among the three proteins. These findings might present RPS3 as a selective molecular marker in colon cancer and an attractive target for colon cancer therapy.
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Affiliation(s)
- Elie Alam
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, P.O.B. 100, Tripoli, Lebanon
| | - Lama Maaliki
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, P.O.B. 100, Tripoli, Lebanon
| | - Zeina Nasr
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, P.O.B. 100, Tripoli, Lebanon.
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Li J, Li W, Wang Z, Khalique A, Wang J, Yang M, Ni X, Zeng D, Zhang D, Zeng Y, Luo Q, Jing B, Pan K. Screening of immune-related differentially expressed genes from primary lymphatic organs of broilers fed with probiotic bacillus cereus PAS38 based on suppression subtractive hybridization. PLoS One 2020; 15:e0235476. [PMID: 32609751 PMCID: PMC7329121 DOI: 10.1371/journal.pone.0235476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/16/2020] [Indexed: 12/18/2022] Open
Abstract
To explore the molecular mechanism of the effect of Bacillus cereus PAS38 on the immunity of broilers, sixty 7-day-old broilers were divided into two groups with three replicates. The control group was fed with basal diet, and the treatment group was fed with basal diet containing Bacillus cereus PAS38 1×106 CFU/g. Thymus and bursa of fabricius were taken from two groups of broilers at the age of 42 days, total RNA was extracted, differential gene library was constructed by SSH technology, and immune-related differential genes were screened. Then, we used siRNA to interfere with the expression of some differential genes in the original generation lymphocytes of broiler blood to detect the change of cytokines mRNA expression level. A total of 42 immune-related differentially expressed genes were screened, including 22 up-regulated genes and 20 down-regulated genes. When 7 differentially up-regulated genes associated with enhanced immune function were interfered with in lymphocytes, some immune-promoting cytokines were down-regulated. These results showed that Bacillus cereus PAS38 might up-regulate the expression of JCHAIN, PRDX1, CD3E, CDK6 and other genes in immune organs of broilers, thereby affecting the development of immune organs, the expression of various cytokines and the transduction of immune signals, improving the immune capacity of broilers.
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Affiliation(s)
- Jiajun Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Wanqiang Li
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Zhenhua Wang
- Branch of Animal Husbandry and Veterinary Medicine, Chengdu Vocational College of Agricultural Science and Technology, Chengdu, Sichuan Province, China
| | - Abdul Khalique
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Junrui Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Miao Yang
- Technology Centre of Chengdu Custom, Chengdu, Sichuan Province, China
| | - Xueqin Ni
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Dong Zeng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Dongmei Zhang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Yan Zeng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Qihui Luo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Bo Jing
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Kangcheng Pan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan Province, China
- * E-mail:
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Cellular Stress Responses in Radiotherapy. Cells 2019; 8:cells8091105. [PMID: 31540530 PMCID: PMC6769573 DOI: 10.3390/cells8091105] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/11/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is one of the major cancer treatment strategies. Exposure to penetrating radiation causes cellular stress, directly or indirectly, due to the generation of reactive oxygen species, DNA damage, and subcellular organelle damage and autophagy. These radiation-induced damage responses cooperatively contribute to cancer cell death, but paradoxically, radiotherapy also causes the activation of damage-repair and survival signaling to alleviate radiation-induced cytotoxic effects in a small percentage of cancer cells, and these activations are responsible for tumor radio-resistance. The present study describes the molecular mechanisms responsible for radiation-induced cellular stress response and radioresistance, and the therapeutic approaches used to overcome radioresistance.
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Chen Z, Xu W. Targeting E3 ubiquitin ligases to sensitize cancer radiation therapy. PRECISION RADIATION ONCOLOGY 2019. [DOI: 10.1002/pro6.1069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Zan Chen
- Department of Cell BiologyHarvard Medical School Boston USA
| | - Wei Xu
- Department of Pharmacology and Molecular SciencesJohns Hopkins University, School of Medicine Baltimore USA
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35
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Do H, Kim D, Kang J, Son B, Seo D, Youn H, Youn B, Kim W. TFAP2C increases cell proliferation by downregulating GADD45B and PMAIP1 in non-small cell lung cancer cells. Biol Res 2019; 52:35. [PMID: 31296259 PMCID: PMC6625030 DOI: 10.1186/s40659-019-0244-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/05/2019] [Indexed: 12/25/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is one of the leading causes of death in the world. NSCLC diagnosed at an early stage can be highly curable with a positive prognosis, but biomarker limitations make it difficult to diagnose lung cancer at an early stage. To identify biomarkers for lung cancer development, we previously focused on the oncogenic roles of transcription factor TFAP2C in lung cancers and revealed the molecular mechanism of several oncogenes in lung tumorigenesis based on TFAP2C-related microarray analysis. Results In this study, we analyzed microarray data to identify tumor suppressor genes and nine genes downregulated by TFAP2C were screened. Among the nine genes, we focused on growth arrest and DNA-damage-inducible beta (GADD45B) and phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1) as representative TFAP2C-regulated tumor suppressor genes. It was observed that overexpressed TFAP2C resulted in inhibition of GADD45B and PMAIP1 expressions at both the mRNA and protein levels in NSCLC cells. In addition, downregulation of GADD45B and PMAIP1 by TFAP2C promoted cell proliferation and cell motility, which are closely associated with NSCLC tumorigenesis. Conclusion This study indicates that GADD45B and PMAIP1 could be promising tumor suppressors for NSCLC and might be useful as prognostic markers for use in NSCLC therapy. Electronic supplementary material The online version of this article (10.1186/s40659-019-0244-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyunhee Do
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, 28173, Republic of Korea
| | - Dain Kim
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, 28173, Republic of Korea
| | - JiHoon Kang
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Beomseok Son
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Danbi Seo
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, 28173, Republic of Korea
| | - HyeSook Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, 05006, Republic of Korea
| | - BuHyun Youn
- Department of Integrated Biological Science, Pusan National University, Busan, 46241, Republic of Korea. .,Department of Biological Sciences, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea.
| | - Wanyeon Kim
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, 28173, Republic of Korea. .,Department of Biology Education, Korea National University of Education, 250 Taeseongtabyeon-ro, Gangnae-myeon, Heungdeok-gu, Cheongju-si, Chungbuk, 28173, Republic of Korea.
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36
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Kang H, Kim H, Lee S, Youn H, Youn B. Role of Metabolic Reprogramming in Epithelial⁻Mesenchymal Transition (EMT). Int J Mol Sci 2019; 20:ijms20082042. [PMID: 31027222 PMCID: PMC6514888 DOI: 10.3390/ijms20082042] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 02/07/2023] Open
Abstract
Activation of epithelial–mesenchymal transition (EMT) is thought to be an essential step for cancer metastasis. Tumor cells undergo EMT in response to a diverse range of extra- and intracellular stimulants. Recently, it was reported that metabolic shifts control EMT progression and induce tumor aggressiveness. In this review, we summarize the involvement of altered glucose, lipid, and amino acid metabolic enzyme expression and the underlying molecular mechanisms in EMT induction in tumor cells. Moreover, we propose that metabolic regulation through gene-specific or pharmacological inhibition may suppress EMT and this treatment strategy may be applied to prevent tumor progression and improve anti-tumor therapeutic efficacy. This review presents evidence for the importance of metabolic changes in tumor progression and emphasizes the need for further studies to better understand tumor metabolism.
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Affiliation(s)
- Hyunkoo Kang
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
| | - Hyunwoo Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
| | - Sungmin Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
| | - HyeSook Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul 05006, Korea.
| | - BuHyun Youn
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
- Department of Biological Sciences, Pusan National University, Busan 46241, Korea.
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Shafi A, Nguyen T, Peyvandipour A, Nguyen H, Draghici S. A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures. Front Genet 2019; 10:159. [PMID: 30941158 PMCID: PMC6434849 DOI: 10.3389/fgene.2019.00159] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/14/2019] [Indexed: 12/20/2022] Open
Abstract
Although massive amounts of condition-specific molecular profiles are being accumulated in public repositories every day, meaningful interpretation of these data remains a major challenge. In an effort to identify the biomarkers that describe the key biological phenomena for a given condition, several approaches have been developed over the past few years. However, the majority of these approaches either (i) do not consider the known intermolecular interactions, or (ii) do not integrate molecular data of multiple types (e.g., genomics, transcriptomics, proteomics, epigenomics, etc.), and thus potentially fail to capture the true biological changes responsible for complex diseases (e.g., cancer). In addition, these approaches often ignore the heterogeneity and study bias present in independent molecular cohorts. In this manuscript, we propose a novel multi-cohort and multi-omics meta-analysis framework that overcomes all three limitations mentioned above in order to identify robust molecular subnetworks that capture the key dynamic nature of a given biological condition. Our framework integrates multiple independent gene expression studies, unmatched DNA methylation studies, and protein-protein interactions to identify methylation-driven subnetworks. We demonstrate the proposed framework by constructing subnetworks related to two complex diseases: glioblastoma and low-grade gliomas. We validate the identified subnetworks by showing their ability to predict patients' clinical outcome on multiple independent validation cohorts.
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Affiliation(s)
- Adib Shafi
- Department of Computer Science, Wayne State University, Detroit, MI, United States
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV, United States
| | - Azam Peyvandipour
- Department of Computer Science, Wayne State University, Detroit, MI, United States
| | - Hung Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV, United States
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, United States.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
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Peng H, Zhao Y, Chen J, Huo J, Zhang Y, Xiao T. Knockdown of ribosomal protein S3 causes preimplantation developmental arrest in mice. Theriogenology 2019; 129:77-81. [PMID: 30826720 DOI: 10.1016/j.theriogenology.2019.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/09/2019] [Accepted: 02/22/2019] [Indexed: 01/05/2023]
Abstract
Ribosomal protein S3 (RpS3), a member of the ribosome 40S subunit, has conventional ribosomal function and additional extraribosomal functions. The aim of the present study was to analyze the expression and localization of RpS3 and its function in early embryogenesis in mice. RpS3 mRNA and protein were expressed in multiple mouse tissues. In the ovary, RpS3 protein was ubiquitously and highly expressed in oocytes and granulosa cells. After ovulation and fertilization, RpS3 mRNA and protein were detected in oocytes and preimplantation embryos. Furthermore, RpS3 protein was localized in the cytoplasm of oocytes and preimplantation embryos. Moreover, knockdown of RpS3 in zygotes led to a significantly decreased rate of blastocyst formation. These results provide the first evidence for a novel function of RpS3 in regulating early embryonic development in mice.
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Affiliation(s)
- Hui Peng
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China; University Key Lab for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare in Fujian Province, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Yifan Zhao
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Jing Chen
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Jianchao Huo
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Yanyan Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Tianfang Xiao
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China.
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SseL Deubiquitinates RPS3 to Inhibit Its Nuclear Translocation. Pathogens 2018; 7:pathogens7040086. [PMID: 30405005 PMCID: PMC6313570 DOI: 10.3390/pathogens7040086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 11/25/2022] Open
Abstract
Many Gram-negative bacterial pathogens use type III secretion systems to deliver virulence proteins (effectors) into host cells to counteract innate immunity. The ribosomal protein S3 (RPS3) guides NF-κB subunits to specific κB sites and plays an important role in the innate response to bacterial infection. Two E. coli effectors inhibit RPS3 nuclear translocation. NleH1 inhibits RPS3 phosphorylation by IKK-β, an essential aspect of the RPS3 nuclear translocation process. NleC proteolysis of p65 generates an N-terminal p65 fragment that competes for full-length p65 binding to RPS3, thus also inhibiting RPS3 nuclear translocation. Thus, E. coli has multiple mechanisms by which to block RPS3-mediated transcriptional activation. With this in mind, we considered whether other enteric pathogens also encode T3SS effectors that impact this important host regulatory pathway. Here we report that the Salmonella Secreted Effector L (SseL), which was previously shown to function as a deubiquitinase and inhibit NF-κB signaling, also inhibits RPS3 nuclear translocation by deubiquitinating this important host transcriptional co-factor. RPS3 deubiquitination by SseL was restricted to K63-linkages and mutating the active-site cysteine of SseL abolished its ability to deubiquitinate and subsequently inhibit RPS3 nuclear translocation. Thus, Salmonella also encodes at least one T3SS effector that alters RPS3 activities in the host nucleus.
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Park G, Son B, Kang J, Lee S, Jeon J, Kim JH, Yi GR, Youn H, Moon C, Nam SY, Youn B. LDR-Induced miR-30a and miR-30b Target the PAI-1 Pathway to Control Adverse Effects of NSCLC Radiotherapy. Mol Ther 2018; 27:342-354. [PMID: 30424954 DOI: 10.1016/j.ymthe.2018.10.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/24/2022] Open
Abstract
Radiotherapy has been a central part in curing non-small cell lung cancer (NSCLC). However, it is possible that not all of the tumor cells are destroyed by radiation; therefore, it is important to effectively control residual tumor cells that could become aggressive and resistant to radiotherapy. In this study, we aimed to investigate the molecular mechanism of decreased NSCLC radioresistance by low-dose radiation (LDR) pretreatment. The results indicated that miR-30a and miR-30b, which effectively inhibited plasminogen activator inhibitor-1 (PAI-1), were overexpressed by treatment of LDR to NSCLC cells. Phosphorylation of Akt and ERK, the downstream survival signals of PAI-1, was decreased by PAI-1 inhibition. Reduced cell survival and epithelial-mesenchymal transition by PAI-1 inhibition were confirmed in NSCLC cells. Moreover, in vivo orthotopic xenograft mouse models with 7C1 nanoparticles to deliver miRNAs showed that tumor growth and aggressiveness were efficiently decreased by LDR treatment followed by radiotherapy. Taken together, the present study suggested that PAI-1, whose expression is regulated by LDR, was critical for controlling surviving tumor cells after radiotherapy.
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Affiliation(s)
- Gaeul Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea
| | - Beomseok Son
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea
| | - JiHoon Kang
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Republic of Korea
| | - Sungmin Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea
| | - Jaewan Jeon
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; Department of Radiation Oncology, Haeundae Paik Hospital, Inje University School of Medicine, Busan 48108, Republic of Korea
| | - Joo-Hyung Kim
- Department of Chemistry, Molecular Design Institute, New York University, New York, NY 10003, USA
| | - Gi-Ra Yi
- School of Chemical Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - HyeSook Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Changjong Moon
- Department of Veterinary Anatomy, College of Veterinary Medicine and BK21 Plus Project Team, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seon Young Nam
- Low-Dose Radiation Research Team, Radiation Health Institute, Korea Hydro & Nuclear Power Co., Ltd., Seoul 01450, Republic of Korea
| | - BuHyun Youn
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; Department of Biological Sciences, Pusan National University, Busan 46241, Republic of Korea.
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Vastrad C, Vastrad B. Bioinformatics analysis of gene expression profiles to diagnose crucial and novel genes in glioblastoma multiform. Pathol Res Pract 2018; 214:1395-1461. [PMID: 30097214 DOI: 10.1016/j.prp.2018.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/27/2018] [Accepted: 07/22/2018] [Indexed: 02/07/2023]
Abstract
Therefore, the current study aimed to diagnose the genes associated in the pathogenesis of GBM. The differentially expressed genes (DEGs) were diagnosed using the limma software package. The ToppFun was used to perform pathway and Gene Ontology (GO) enrichment analysis of the DEGs. Protein-protein interaction (PPI) networks, extracted modules, miRNA-target genes regulatory network and miRNA-target genes regulatory network were used to obtain insight into the actions of DEGs. Survival analysis for DEGs carried out. A total of 701 DEGs, including 413 upregulated and 288 downregulated genes, were diagnosed between U1118MG cell line (PK 11195 treated with 1 h exposure) and U1118MG cell line (PK 11195 treated with 24 h exposure). The up-regulated genes were enriched in superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis, cell cycle, cell cycle process and chromosome. The down-regulated genes were enriched in folate transformations I, biosynthesis of amino acids, cellular amino acid metabolic process and vacuolar membrane. The current study screened the genes in PPI network, extracted modules, miRNA-target genes regulatory network and miRNA-target genes regulatory network with higher degrees as hub genes, which included MYC, TERF2IP, CDK1, EEF1G, TXNIP, SLC1A5, RGS4 and IER5L Survival suggested that low expressed NR4A2, SLC7 A5, CYR61 and ID1 in patients with GBM was linked with a positive prognosis for overall survival. In conclusion, the current study could improve our understanding of the molecular mechanisms in the progression of GBM, and these crucial as well as new molecular markers might be used as therapeutic targets for GBM.
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Affiliation(s)
- Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, 580001, Karanataka, India.
| | - Basavaraj Vastrad
- Department of Pharmaceutics, SET`S College of Pharmacy, Dharwad, Karnataka, 580002, India
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